The Complete Chloroplast Genomes of Echinacanthus Species (Acanthaceae): Phylogenetic Relationships, Adaptive Evolution, and Screening of Molecular Markers

Abstract

Among the four species of Echinacanthus (Acanthaceae), one distributed in the West Himalayan region and three restricted to the Sino-Vietnamese karst region. Because of its ecological significance, molecular markers are necessary for proper assessment of its genetic diversity and phylogenetic relationships. Herein, the complete chloroplast genomes of four Echinacanthus species were determined for the first time. The results indicated that all the chloroplast genomes were mapped as a circular structure and each genomes included 113 unique genes, of which 80 were protein-coding, 29 were tRNAs, and 4 were rRNAs. However, the four cp genomes ranged from 151,333 to 152,672 bp in length. Comparison of the four cp genomes showed that the divergence level was greater between geographic groups. We also analyzed IR expansion or contraction in the four cp genomes and the fifth type of the large single copy/inverted repeat region in Lamiales was suggested. Furthermore, based on the analyses of comparison and nucleotide variability, six most divergent sequences (rrn16, ycf1, ndhA, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, and psaA-ycf3) were identified. A total of 37–45 simple sequence repeats were discovered in the four species and 22 SSRs were identified as candidate effective molecular markers for detecting interspecies polymorphisms. These SSRs and hotspot regions could be used as potential molecular markers for future study. Phylogenetic analysis based on Bayesian and parsimony methods did not support the monophyly of Echinacanthus. The phylogenetic relationships among the four species were clearly resolved and the results supported the recognition of the Sino-Vietnamese Echinacanthus species as a new genus. Based on the protein sequence evolution analysis, 12 genes (rpl14, rpl16, rps4, rps15, rps18, rps19, psbK, psbN, ndhC, ndhJ, rpoB, and infA) were detected under positive selection in branch of Sino-Vietnamese Echinacanthus species. These genes will lead to understanding the adaptation of Echinacanthus species to karst environment. The study will help to resolve the phylogenetic relationship and understand the adaptive evolution of Echinacanthus. It will also provide genomic resources and potential markers suitable for future species identification and speciation studies of the genus.

Complete Chloroplast Genomes of Three Medicinal Alpinia Species: Genome Organization, Comparative Analyses and Phylogenetic Relationships in Family Zingiberaceae

“…The most abundant were mononucleotide repeats, located in non-coding regions, and contributed to AT richness ( Figure 3). These results are consistent with most reported angiosperms [23][24][25][26][28][29][30]. The total number of SSRs was 237 in A. katsumadai, 244 in A. oxyphylla sampled from Guangdong, 247 in A. pumila, 236 in A. zerumbet, and 241 in A. oxyphylla sampled from Hainan ( Figure 3A).…”

“…The contractions and expansions at the borders of IR regions were common evolutionary events and may cause size variations of chloroplast genomes [13,[23][24][25][26][27][28][29][30]. We compared the IR-SC boundaries information of the five Alpinia chloroplast genomes ( Figure 5).…”

“…Typical chloroplast genomes of angiosperms have a generally conserved quadripartite circular structure, which consists of a large single copy (LSC) region, a small single copy (SSC) region, and two copies of inverted repeats (IRs) [16][17][18]. With the rapid development of high-throughput sequencing technologies, such as Illumina and PacBio sequencing platforms, it is now convenient to acquire complete chloroplast genome sequences [19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34]. The chloroplast genomes have been widely utilized for species identification, the reconstruction of phylogenetic relationships, the resolution of origin problems, and the development of molecular markers [19][20][21][22][23][24][25][26][27][28][29][30].…”

Exploring evolution characteristic between cultivated tea and its wild relatives using complete chloroplast genomes

“…First, to have a clear view of the cp genomic adaptative evolution of cultivated tea, we did evolution analysis on proteincoding sequence. The Ka/Ks ratio is very useful for measuring selective pressure at the protein level [35]. In this study, Ka/Ks value of 79 genes are 0, and the only rpoB is 0.3004.…”

“…They were also under selective pressure in beverage crops [36]. rps15 gene have function in chloroplast ribosome subunits [35]. ycf1, encoding a component of the chloroplast's inner envelope membrane protein translocon, is one of the largest plastid genes [36], and is also essential for almost all plant lineages [37].…”